+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10573 | |||||||||
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Title | Ovine ATP synthase 1a state | |||||||||
Map data | Composite map of state 1a of ovine F1Fo, obtained from series of focused refinements as described in the paper. | |||||||||
Sample |
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Keywords | ATP synthase / mitochondrial / respiratory chain / mammalian / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information negative regulation of cell adhesion involved in substrate-bound cell migration / ATP biosynthetic process / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / cellular response to interleukin-7 / proton-transporting ATP synthase complex / : / : ...negative regulation of cell adhesion involved in substrate-bound cell migration / ATP biosynthetic process / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / cellular response to interleukin-7 / proton-transporting ATP synthase complex / : / : / : / Mitochondrial protein degradation / MHC class I protein binding / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / positive regulation of blood vessel endothelial cell migration / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / monoatomic ion transport / proton-transporting ATPase activity, rotational mechanism / aerobic respiration / proton-transporting ATP synthase activity, rotational mechanism / regulation of intracellular pH / mitochondrial membrane / lipid metabolic process / angiogenesis / mitochondrial inner membrane / lipid binding / cell surface / mitochondrion / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Ovis aries (sheep) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Pinke G / Zhou L | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Cryo-EM structure of the entire mammalian F-type ATP synthase. Authors: Gergely Pinke / Long Zhou / Leonid A Sazanov / Abstract: The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain ...The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the 'proton translocation cluster' attached to the c-ring and a more distant 'hook apparatus' holding subunit e. Unexpectedly, this subunit is anchored to a lipid 'plug' capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10573.map.gz | 3.2 MB | EMDB map data format | |
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Header (meta data) | emd-10573-v30.xml emd-10573.xml | 31.6 KB 31.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10573_fsc.xml | 15.3 KB | Display | FSC data file |
Images | emd_10573.png | 129.8 KB | ||
Masks | emd_10573_msk_1.map | 307.5 MB | Mask map | |
Filedesc metadata | emd-10573.cif.gz | 8.8 KB | ||
Others | emd_10573_additional_1.map.gz emd_10573_additional_2.map.gz emd_10573_additional_3.map.gz emd_10573_half_map_1.map.gz emd_10573_half_map_2.map.gz | 245.5 MB 245.6 MB 1.5 MB 245.9 MB 245.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10573 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10573 | HTTPS FTP |
-Validation report
Summary document | emd_10573_validation.pdf.gz | 250.5 KB | Display | EMDB validaton report |
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Full document | emd_10573_full_validation.pdf.gz | 249.6 KB | Display | |
Data in XML | emd_10573_validation.xml.gz | 11.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10573 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10573 | HTTPS FTP |
-Related structure data
Related structure data | 6tt7MC 6za9C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10573.map.gz / Format: CCP4 / Size: 16.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite map of state 1a of ovine F1Fo, obtained from series of focused refinements as described in the paper. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.061 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10573_msk_1.map | ||||||||||||
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-Supplemental map: emd 10573 additional 1.map
File | emd_10573_additional_1.map | ||||||||||||
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Density Histograms |
-Supplemental map: emd 10573 additional 2.map
File | emd_10573_additional_2.map | ||||||||||||
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Density Histograms |
-Supplemental map: emd 10573 additional 3.map
File | emd_10573_additional_3.map | ||||||||||||
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Density Histograms |
-Supplemental map: emd 10573 half map 1.map
File | emd_10573_half_map_1.map | ||||||||||||
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Density Histograms |
-Supplemental map: emd 10573 half map 2.map
File | emd_10573_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Purified ATP synthase from sheep heart mitochondria
+Supramolecule #1: Purified ATP synthase from sheep heart mitochondria
+Macromolecule #1: ATP synthase subunit alpha
+Macromolecule #2: ATP synthase subunit beta
+Macromolecule #3: ATP synthase subunit gamma
+Macromolecule #4: ATP synthase F1 subunit delta
+Macromolecule #5: ATP synthase F1 subunit epsilon
+Macromolecule #6: ATP synthase peripheral stalk subunit OSCP
+Macromolecule #7: ATP synthase subunit b
+Macromolecule #8: ATP synthase-coupling factor 6, mitochondrial
+Macromolecule #9: ATP synthase subunit d, mitochondrial
+Macromolecule #10: ATP synthase F(0) complex subunit C1, mitochondrial
+Macromolecule #11: ATP synthase subunit a
+Macromolecule #12: Subunit DAPIT
+Macromolecule #13: ATP synthase membrane subunit 6.8PL
+Macromolecule #14: ATP synthase protein 8
+Macromolecule #15: ATP synthase membrane subunit f
+Macromolecule #16: ATP synthase subunit
+Macromolecule #17: Subunit e
+Macromolecule #18: MAGNESIUM ION
+Macromolecule #19: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #20: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #21: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...
+Macromolecule #22: CARDIOLIPIN
+Macromolecule #23: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}p...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.8 mg/mL |
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Buffer | pH: 7.4 Details: 20 mM HEPES pH7.4, 35 mM NaCl, 2 mM EDTA, 1% sucrose, 1 mM DTT, 0.1% LMNG, 0.2% CHAPS |
Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3053 / Average exposure time: 1.0 sec. / Average electron dose: 106.0 e/Å2 / Details: 40 frames per movie |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.4 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 131951 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL |
Output model | PDB-6tt7: |